Hi Bruce, Thank you for this quick check. Your results confirm my suspicion: "aparc.a2005s+aseg.mgz" does not have this wm-label. So, after trying every segmentation file I found in /mri (aparc+aseg.mgz, wmparc.mgz, aparc.a2005s+aseg.mgz) without success, I asked me
Where can I find or how can I create the necessary segmentation volume to extract 3136 or 4181? Somebody has an idea? kind regards, Markus -----Ursprüngliche Nachricht----- Von: Bruce Fischl [mailto:[EMAIL PROTECTED] Gesendet: Mittwoch, 10. Dezember 2008 19:16 An: Markus Röhl Betreff: Re: AW: AW: [Freesurfer] mri_extract_label 4181 Hi Markus, are you sure there is a 3136 in the data? That is a wm label, and is probably in the wmparc.mgz, not this one. The 1136 is the ctx label. I did: matlab >> [v,M,mr] = load_mgh('aparc.a2005s+aseg.mgz'); >> find(v(:) == 3136) ans = Empty matrix: 0-by-1 >> find(v(:) == 1136) ans = 4607151 4672429 4672430 4672687 4672944 4737453 4737708 4737709 4737963 4737965 4737966 4737967 . . . On Wed, 10 Dec 2008, Markus Röhl wrote: > Hi Bruce, > > the command line that fails is: > > mri_extract_label ./aparc.a2005s+aseg.mgz 3136 ./test.nii.gz > > This works fine: > > mri_extract_label ./aparc.a2005s+aseg.mgz 1136 ./test2.nii.gz > > Best regards, > > Markus > > -----Ursprüngliche Nachricht----- > Von: Bruce Fischl [mailto:[EMAIL PROTECTED] > Gesendet: Mittwoch, 10. Dezember 2008 18:38 > An: Markus Röhl > Betreff: Re: AW: [Freesurfer] mri_extract_label 4181 > > Hi Markus > > can you email me the aparc.a2005s+aseg.mgz and the exact command line > that fails? > Bruce > On Wed, 10 Dec 2008, Markus Röhl wrote: > >> Hi >> >> for the purpose of illustration I change to >> >> 3136 wm-lh-G_temp_sup-Planum_tempolare >> >> The corresponding gray matter part (1136) can seen in cortex.tiff. It is >> labeled green and can be found quite in the middle of the picture right > from >> the red labeled S_temporal_transverse. The successful extraction of the > 1136 >> ctx-lh-G_temp_sup-Planum_tempolare is shown in success.png. >> >> The corresponding white matter of this landmark (3136 >> wm-lh-G_temp_sup-Planum_tempolare) can also be seen on the right side of >> WM.tiff as a green labeled area superior of the pink labeled lateral > aspect >> of G_temp_sup. (the 3181 wm-lh-S_temporal_transverse is also present as a >> very very small red labeled area between the small blue and green areas in >> the middle of WM.tiff). >> >> I am not able to extract 3136 and I think this seems to hold also for the >> other 3XXX or 4XXX wm-labels from aparc.a2005s+aseg.mgz. >> >> I extracted 2034 ctx-rh-transversetemporal from "aparc+aseg.mgz" and > analog >> 4034 wm-lh-transversetemporal from "wmparc.mgz". I assumed that there must >> be a corresponding file of "aparc.a2005s+aseg.mgz" like >> "wmparc.a2005s+aseg.mgz" to extract white matter labels. >> "aparc.a2005s+aseg.mgz" seems to work only for ctx- but not for wm-labels, >> and I don't found something else. The problem is not subject-related. >> >> Regards, >> >> Markus >> >> >> -----Ursprüngliche Nachricht----- >> Von: Christophe Destrieux [mailto:[EMAIL PROTECTED] >> Gesendet: Mittwoch, 10. Dezember 2008 14:24 >> An: Bruce Fischl >> Cc: Markus Röhl; freesurfer@nmr.mgh.harvard.edu >> Betreff: Re: [Freesurfer] mri_extract_label 4181 >> >> Hi Bruce and Markus >> >> S_temporal_transverse is constant and should be present on the surface ; >> >> cheers >>> HI Markus, >>> >>> that's one of Christophe's labels, so would only be in the >>> aparc.a2005s+aseg.mgz. Have you cheched the aparc.a2005s.annot on the >>> surface to verify that it is present there? There are also some labels >>> that don't appear on every subject, Christophe would know if this is >>> one of them. >>> >>> cheers, >>> Bruce >>> >>> On Wed, 10 Dec 2008, Markus Röhl wrote: >>> >>>> Dear all, >>>> >>>> I used mri_extract_label recently to get NIfTI -binary maps for certain >>>> anatomical landmarks, e.g. the Gyrus temporalis inferior of the left >>>> hemisphere (cortex) which index is listed in FreeSurferColotLUT.txt: >>>> >>>> mri_extract_label $FREESURFER_HOME/subjects/VP1/mri/aparc+aseg.mgz 1009 >>>> $FREESURFER_HOME/subjects/ROI/VP1/CL_IT.nii.gz >>>> >>>> This works fine. Now I want to extract the labels of anatomical >>>> landmarks >>>> like >>>> >>>> 4181 wm-rh-S_temporal_transverse >>>> >>>> I tried every segmentation file I found (aparc+aseg.mgz, wmparc.mgz, >>>> aparc.a2005s+aseg.mgz), but only ended up with empty maps. Where I >>>> can find >>>> or how can I create the necessary segmentation volume? >>>> >>>> Regards, >>>> >>>> Markus >>>> >>>> >>>> >>>> >> >> >> > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
